I always run a CHKDSK when trying to determine whether or not a harddrive is going bad, or if it's just simply files that are in error. If you're unsure of how to run this, open your Run command line (windows key+r, Win7), and type in CMD. After pressing the Enter key, you'll be greeted by a black background window with white text. In here, type the above CHKDSK /F (the /F stands for Fix) and press Enter. It will likely require you to restart your computer, and will ask if you want to schedule the CHKDSK after the restart, and before your OS and other programs load. Select yes (Press Y and hit Enter), and then restart your computer.
Whether or not the file structure is messed up, or whether or not there's other diagnostics it tries to run, will determine how much time the scan will take. But this can be a reliable way to help narrow down your issue.